The important things to notice in this case are the green and yellow texture axis lines. When you scale negative, the axis doesn't change, but when you align to face, the axes are rotated so that they are flat against the face in a certain direction. Notice that the green axis doesn't move but the yellow one is flipped. This means that the texture normal has been rotated to face outwards relative to the face rather than inwards.
Unfortunately you can't manipulate the texture axis directly, apart from these three operations:
Rotate the texture (only rotates on the XY axis, you can't adjust Z)
Align to face/world (limited to only two different axis positions)
Alt+Right Click (dependant upon the last selected face)
In an ideal world you would be able to choose the normal vector of the texture axes, but typically you don't need to, as it would usually result in stretched textures, and that kind of control isn't really necessary. You can always cheat by rotating your brush a bit, turning texture lock off, and rotating it back. At least I think that works.
Sorry, I went on for a bit there.